Pepper variome reveals the history and key loci associated with fruit domestication and diversification.

Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.

Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.).

The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F2 and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200-250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.

Photosynthetically active radiation and carbon gain drives the southern orientation of Myrtillocactus geometrizans fruits.

The equatorial orientation of reproductive structures is known in some columnar cacti from extratropical deserts. It has been hypothesised that photosynthetically active radiation (PAR) interception is the main reason for this orientation, because of its key effect on nocturnal CO2 uptake. However, there are no studies addressing both the effect of PAR and its consequence, carbon gain, on fruit orientation. Accordingly, we tested whether PAR and carbon gain could explain the southern fruit orientation of Myrtillocactus geometrizans, an inter-tropical columnar cactus. We studied three populations of M. geometrizans in Mexico. For each population, azimuth of fruits, total daily PAR, nocturnal acid accumulation (NAA) and fruit production were measured. The relationships between rib orientation and number of fruits, as well as total daily PAR, were evaluated using periodic regressions. The effect of total daily PAR and NAA on number of fruits was assessed using generalised linear models. During spring, mean fruit orientation had a south azimuth for three populations. Likewise, rib orientation had a significant effect on fruit production, with the south-facing ribs having the maximum number of fruits. Total daily PAR was highest in the south-facing ribs, at least for those in the northern and central populations. Furthermore, during spring, there was a significant positive effect of total daily PAR and NAA on fruit production. Our results provide strong evidence that the higher carbon gain in equatorial ribs, through a highest interception of PAR, would be the responsible factor for equatorial orientation of fruits in an inter-tropical columnar cactus.